Figure 2

Classification of S/T phosphorylation sites into general kinase recognition sequence categories. At present, not all consensus phosphorylation motifs are known for all kinases. A number of general phosphosite classes have been annotated based on amino acid sequences surrounding S/T phosphorylation sites: proline-directed, acidic, basic and otherwise [97]. (a-c) Sequence logos for Polycomb Group (PcG) phosphorylation motifs of proline-directed ((a), n = 42) acidic ((b), n = 36) and basic ((c), n = 15) categories where the phosphorylated residue (S/T) is centered were generated with Weblogo [98]. Only serine and threonine phosphorylation sites were taken into account when a full 15-mer sequence was available. To avoid sequence bias only non-overlapping human and mouse PcG phosphorylation sites were used. Centered 15-mer sequences were assigned to a motif class sequentially by following a binary decision tree as follows: P at +1 (Pro-directed), 5 or more E/D at +1 to +6 (acidic), R/K at -3 (basic), D/E at +1/+2 or +3 (acidic), 2 or more R/K at -6 to -1 (basic), otherwise. Colors correspond to the chemical properties of the amino acids: hydrophobic (black), basic (blue), acidic (red) and polar (green). (a) Although phosphosite numbers are low and thus no solid deductions are warranted, it is apparent for the proline-directed class (classified by a P in the +1 position), that prolines are not limited to +1, but are abundant in various - and + positions. (b) In the acidic motif, characterized by the presence of the amino acids glutamic acid (E) and aspartic acid (D) in the + residues, E/Ds are present in the - positions. (c) In basic motifs, arginine (R) is predominantly found in -3 positions, in addition to -5.